Chuck vs The Aftermath
by s1nn3r
Summary: Malibu always looked beautiful this time of day as the sun started to set, two people destined to be together must make some tough choices. Picks up right after the ending to vs The Goodbye.
1. Chapter 1

_**~~This is my first attempt at a fanfiction story. I appreciate any feedback and welcome any criticism so that I can improve this story for you, the readers.**_

 _ **~~I know you have read so many follow-ups to vs The Goodbye, but I really wanted to an interpretation and I hope you enjoy it. I do not own Chuck or any of the characters portrayed in this story.**_

 **Chapter 1 - Chuck vs The Aftermath**

The sand glistened off the water as the sun started to set on the horizon, time had seemed to slowly tick by, yet the day was almost gone. Sarah and Chuck just sat in silence staring out the water, watching the gentle waves slowly roll in then recede as the orange and red glow from the day coming to a close bounced perfectly off the reflection in the water. The air turned chilly, well as chilly as one can get in Malibu.

Chuck was thankful he pursued Sarah and had this day with her, reliving their story and seeing her expressions as she heard it for the first time. He shared each powerful moment that had led them to the present or as much as he could remember. He was overjoyed just to have Sarah sit and listen and as he stared at the gorgeous blonde, he realized that even if he never saw her again after this he would always have this day, this perfect moment with woman he had given his entire heart to. As he finished speaking he saw the moment over and over in his head where Sarah in a way that showed she still cared for him said, Kiss me. He would have to give Morgan credit that even if his idea didn't work it created this perfect moment.

Sarah lost in her head trying to piece together fragments of the story, leaning softly on Chuck's shoulder and trying to decide how she wanted to proceed. She felt so many overwhelming feelings, but had no idea how to handle what she experiencing. She knew little of this man past what he had told her, but still she felt close to him. She looked up at Chuck and slowly began to study why she fell for such a man, he was strong, caring, compassionate, gentle, and very attractive. She could tell this just from the brief time she had spent with him after she had hunted down Quinn, only to have to flee after discovering what he was ultimately after and then asking Chuck to help her locate Quinn before he pushed his way into her mission. She thought about the brief recalls she had almost like a subconscious reflex at the stacking order of some cups at a random fast food store that Chuck said she worked at as a cover job, about Irene Demova, and saving the General and everyone in that concert hall. Most of all, the carving at that house, which had saved her from completely losing both this very special man and herself. She didn't know where these small fragments of ideas she didn't recall came from, but that gave her hope, even if it terrified her. Suddenly, she felt an arm around her pulling her closer, just that warming gesture made her feel safe in the arms of this person that she felt close to. She was still processing when she felt something inside her pull back; whether it was the fact she was a spy, the daughter of a conman, they both taught her feelings like this were being weak. So, she slowly pulled Chuck's arm off her and gingerly stood up. As Chuck rose with a look that she could only describe as fearful yet hoping that she could be somebody she wasn't, she look down at the sand as it had almost turned to nightfall, the grains taking on an almost blackened appearance, which matched how she needed to feel to do what came next and spoke.

"Chuck, I really appreciate everything you shared with me about our time together and the incredibly crazy story of the past five years, but.."

As she spoke that word he could immediately sense that this wouldn't go the way he had prayed and hoped, that his wife would stay and try to rebuild what they had, but he would be strong for her and accept whatever choice she made. However, deep inside he was a mess of emotions and that same scared guy that had been destroyed by his best friend and ex-girlfriend, and felt he had no future without her. He knew he had grown a lot and hardened as a spy should, but he still felt every emotion the human body could experience with that one word.

"Sarah," Chuck sighed as he interrupted her midsentence, "Before you finish just know that whatever choice you make from here, I will.. I mean I won't interfere. If you need to go I.." He couldn't finish the sentence it hurt too much as he slowly stared at a spot in the sand, tears slowly ran down his face as he watched them fall on the soft grains under his feet.

Sarah interjected as she could tell he was in a lot of pain, "Chuck. I just don't know who I am right now; I lost five years of life. All I can remember is being a spy and focusing on my next mission. I almost killed you and your sister because someone manipulated me, I can't forgive myself for that. Besides, I don't know anything about what you have told me today, but I need time Chuck. I can tell why I fell for you, but I don't feel it. I'm sorry Chuck, but it is best if I spend some time sorting things out on my own."

She looked up in his big brown eyes as he took in every word and she knew that she needed to go, she needed to find some answers for herself and Chuck was only going to complicate things further. Chuck wiped his eyes and gave a small Bartowski smile, he promised that he would be there for her no matter what, and he meant it. "I understand..Sarah remember what I said, you can call..anytime." He heard the words come out of his mouth, but deep down he hated himself for not fighting harder, for not doing everything to make his Sarah come back, but knew that pushing her would not help anything. He hoped she would find the answers she needed and that he could deal with his wife being gone for any period of time.

Sarah gave a small smile and touched his face as she turned to walk towards her Lotus. Chuck watched as she slowly got further and further away from him, she never turned back to take one last look at him, it already hurt so much to do this to him. As Chuck stood in the sand as the night overtook him he knew that he would never give up on her, hell it was in his vows for God's sake. He thought back to their wedding day and the no-vows speech he gave.

" _Sarah. I can't express the depth of my love for you, or my dreams for our future._ _Or the fact that I will fight for you every day._ _Or that our kids will be like little superheroes with little capes and stuff like that. Words can't express that. They just don't cut it. So no vows. I'll just prove it to you every day for the rest of our lives._ _You can count on me."_

The words echoed through his head as he slowly made his way towards his herder, "You can count on me count, Sarah." He quietly whispered to himself.


	2. Chapter 2

_**~~Thank you so much for the feedback and reviews guys, you're the best and I am going to make sure I do this story justice to give everyone a realistic and unique closure.**_

 _ **~~It has been a long time since I have been this obsessed with a show, watched it straight through 3 times and fell in love with the world. I did enjoy the ending, but like everyone else wanted more. I do not own Chuck or any of the characters portrayed in this story.**_

 **Chapter 2 – The Moon**

The drive back to Burbank was somber and almost haunting as his brown eyes were wandering, lost in his own thoughts, trying to comprehend all that had happened. He felt so close to his angel, yet she felt so far away. He had worn his heart on his sleeve for five years for this woman, fought through impossible odds, and fell in and out of love with her more times than he could count. Every time he tried to move on and convince himself they would never be nothing more than asset and handler, something drew him back. He hated that term now – asset; he had been treated as an object, a piece of government technology, and rarely humanized in those first couple years working with the government. He was so concerned if he said the wrong thing that they would just throw him in a bunker or worse that he just accepted their terminology. He never asked for any of this, but threw himself headfirst into fights no normal man without proper training should ever have to be a part of.

Then after he had finally won her heart or maybe he had always had it, he had to slowly and carefully peel back her protective layers to get the sweet caring goddess inside. Chuck thought about all he endured for her and how much each step hurt when he was never truly with her. How could he put all this emotion into winning her back again it was so exhausting last time, he immediately pushed that thought out of his mind. "This is my wife and a person that I will fight every day until I am old and grey for, get a hold of yourself, Chuck."

He tried to talk himself down as he continued to spiral in his own head. He noticed the turnoff for Burbank as he merged into the right lane, dreading what awaited him at their apartment, emptiness, the harsh lonely reality that Sarah wasn't with him. He wondered where she might go and how soon she would call him; again all he could do is wait and give her space. As he looked up at the moon, he pulled into Echo Park wondering if Sarah was staring at that same moon right now, it made him feel a little closer to her, "Come back to me, Sarah." He whispered, sighed and turned off the engine of his herder.

 _ **Viceroy Santa Monica – 10:00 PM**_

The breeze blew in from the open window of her hotel room, as she stared out the gigantic full moon in front of her she hoped Chuck was staring at that same moon, it was so beautiful. Her mind flashed back to the events of a few days before in her room. She had thrown Quinn out the window and held him by a sheet, that lying creep had ruined her life and stolen the last five years from her. The same window that was now fixed with no trace of the vicious engagement she had with him just days before. She wished she had just dropped him off the building then, why had she believed him, because he had a video and some crap story, how could she have been so stupid. As she looked around her hotel room and saw that everything had been cleaned and fixed to its original condition, the CIA had to be keeping tabs on this place and Chuck did say she lived with him and they were married, so why had they kept this room for her?

The blonde hair goddess's mind continued to wander as she slowly paced around her room, she saw her suitcase sitting in the corner, the one she had been living out of the past few days since waking up, she remembered when searching for those glasses for that bastard that the majority of her stuff was at Chuck's apartment. "This will have to do for now, maybe I can go shopping for some new things. I'll have to check my old accounts tomorrow." She went back to the window, after pouring herself a glass of pinot from her refrigerator and just stared at the moon and thoughts about all the stories Chuck had told her, about their story. Some of it was so fantastical that she couldn't believe it was true, but as far as she knew Chuck hadn't lied to her yet, so why would he now.

She thought about how funny it was that he was just a guy who worked at an electronics store before all this and all the sudden he was saving the world with two highly trained spies, "Sounds like the plot of some cheesy TV show." She started cracking up at this thought, as she had a very therapeutic laugh at the absurdity of it all. She thought about one particular mission Chuck had mentioned, it was about Triads and a Chinese restaurant called the Golden Dragon, she recognized this name from somewhere, "Golden Dragon, he said it was close, maybe I can remember something if see it and I am quite hungry." She made up her mind to check it out, looked up the address on her phone, as she unlocked her phone she noticed she had a new text. As she opened the message she got a huge shock that rocked her to her core, "Why didn't Chuck mention this?"


	3. Chapter 3

_**~~Thanks for sticking with the story guys, a lot of the intro here is them examining their feelings for each other, the next chapters will be quite a bit longer and the humor and dialogue will start to open up more going forward.**_

 _ **~~I do not own Chuck or any of the characters portrayed in this story.**_

 **Chapter 3 – The Past Revealed**

 _ **Echo Park – 7:00 AM**_

Chuck had gotten in the habit of running with wife every morning and decided that maybe it will help take his mind off of some of the more obvious things that were bothering him. He slipped into an old white t-shirt and sweatpants as he grabbed a pop tart on the way out the door, he hadn't slept well at all the previous night, but a few cups of coffee had given him enough energy to go out for a run, even though he felt empty and so lonely. All he wanted to do was crawl back in bed and go to sleep, but Sarah would have wanted him to stay strong and he wasn't going to go into depressed zombie cheeseball-crazed Chuck this time. He wondered how Sarah slept or where she was, she probably went back her hotel room he thought as it was quite late when they departed Malibu. Who knows where she would be off to today?

As he was running past the fountain he noticed Alex and Morgan doing stretches with what he thought were yoga mats in the front walkway. They were just getting through doing the warrior's pose as they both saw him running across the courtyard.

"Chuck, how is it going, just getting my stretch on," he stated proudly as he motioned to Chuck. Chuck then slowed his pace and approached them, dreading having to talk about his wife in his current state.

"Hey buddy! Wow Alex, I have never seen Morgan out of his dungeon this early and you got him to actually exercise. Keep this up Morgan and you may make adulthood yet." Chuck quipped as he watched them drop their pose.

"Haha Chuck, Alex just wanted some company and I figured my beautiful girlfriend was worth it, I have to admit that she had to flip my mattress this morning to get me up, but a promise is a promise." Morgan chuckled lightly as Chuck could tell he was still half asleep. "Aww Morgan, always so sweet, I hope you didn't your head too hard this morning. Us Casey's don't mess around when we set our mind to something," Alex said as she gave a pouty look with a mischievous twinkle in her eye.

Morgan rolled his eye as he turned towards Chuck, "So how did operation fairytale go yesterday?" Morgan wanted to gauge Chuck's reaction before deciding how to proceed.

Chuck tried to hide the pain he was feeling as he spoke with his best friend, "She left.." after a long pause he looked up brightly, "I mean she needs space, but we did have a fantastic kiss at sunset, so that's something..?" Chuck trailed off as he slowly hung his head. Chuck lightly brushed his fingers over lips as he thought of how special that kiss was to him, for that brief moment he felt he had his wife back. He wanted that moment to linger for eternity if he never got his Sarah back.

Morgan could feel his friend slowly start to break as the emotional walls started to crumble. "Hey buddy; it will be alright that girl loves you more than anything, even something as crazy as memory loss won't keep you guys apart." He let out a slow breath as he continued. "You are also one of the best spies in the world, with a super computer in your head, no less, and nothing can stop you from getting her memories back," Morgan sounding more and more confident as he spoke.

Chuck eyes started watering as that sadness he felt inside turned to hate, he hated how he had to choose the intersect to diffuse the bomb that Quinn had planted to kill everyone in the concert hall including his loved ones. Because of that choice where there was only one real option, he was unable to restore his wife's memories with the key. Sure it held tremendous power and made you feel like you could do anything. It had also led him to his wife and Casey, him becoming a spy, and actually making a difference in the world. They had done a lot of good together, put away a lot of terrible people that would like nothing more than to watch the world burn and General Beckman did say they were best spy team in the world. However, Sarah herself said he didn't need the intersect to be great. He kept spiraling further and further, lost in his own thoughts.

As he snapped out of his fog and look at his best friend, no matter what happened Morgan always had that positivity about him, "I know buddy, it's going to be a long difficult road back, but we will always find each other and no way am I giving up this time." Chuck gave a sly grin as he truly believed this and after his run he needed a plan, he was going to give Sarah the space she requested, but he would never stop searching for answers. He believed he knew just the place to start, this day just got a lot more exciting.

 _ **Santa Monica Viceroy – 8:00 AM**_

Sarah was in tears as she stared at the name that was displayed on her screen, a text from her mother? She kept reading it; she hadn't slept at all since this realization. She lay awake all night, millions of thoughts and scenarios running her head.

How could this be, she had no way to contact her and it was best for the baby if she only used the low frequency transmitter to warn them if her former handler had discovered their whereabouts. However, there it was plain as day on her screen, _I enjoyed our visit last week honey, stay safe. Molly and I love you._

She couldn't stop the tears from flowing as she pushed her brain as hard as she could to remember what happened, were they actually safe, what did that mean for Ryker. Why had Chuck not told her sooner, maybe they weren't safe and he was protecting them or he didn't think she was equipped to deal with this information yet? She needed answers and she wasn't going to wait around, she had used Castle before when she needed information on Quinn, but she didn't want to risk running into Chuck right now.

 _ **Burbank Buy More**_

Sarah strided in as the automatic glass doors opened, she saw the store was being remodeled, noticed a large Subway sign overhanging in the back of the store and a bunch of employees in green shirts standing around in a circle gazing in aww at some new sandwich that was proudly displayed on the sign. She didn't have time for this as she took this as an opportunity to go into the home theater room and down through the trap door in the floor. She had found her ID badge in her suitcase along with a few other things, so she wouldn't need to ask Chuck to get her into the ex-CIA facility. After clearing the scanner she went down into the old base with the large Carmichael Industries sign still proudly displayed on the wall.

She lingered over the sign as her fingertips brushed across the brush metal finish, Chuck said they built this company together and she was his inspiration. This man that she hardly knew, he had such a good heart, she didn't deserve him. Then as fast as the thought entered her head it is disappeared, she had a purpose and she needed to focus right now. The lights came on and the computers booted up as she reach the bottom of the stairs.

She went to one of the monitors and began to search for information on Ryker, she was trying to remain calm, but inside she was incredibly scared that he might track them down and do who knows what to one person she still really cared for and that baby that it felt like just yesterday she had taken to her mother to raise as her daughter. She searched open cases on the central database, and then she logged in and checked her CIA login to see if it was still active. "Damn, locked out, now what do I do?" She was trying to remain resolute, but that was quickly breaking.

Every moment she wasn't in control of this situation she was slowly losing it. She had always kept them a secret from everyone, no one knew who or where they were. She thought back to that crying baby and the few days hiding from Ryker that she had to care for that baby. She had felt so many emotions in those few days, but right now this was definitely topping it. She needed to make contact; she didn't even know if General Beckman knew about Ryker, this mission was directly from Graham and off the books. Also, she had gone against an order from her handler. "A good spy always does what she is told," Sarah always repeated this to herself in moments of moral dilemma, it helped her shift the blame when she had to do something horrible that the Agency required of her. She knew whatever she did, she needed to be careful Ryker could be watching her or her family's movements and she might know just the person to help.


End file.
